R: Make Node or Edge Graph Features

graph.feature {linkcomm} | R Documentation

## Make Node or Edge Graph Features

### Description

This function returns vectors of node sizes or edge widths for use in `plot.linkcomm`.

### Usage

    graph.feature(x, type = "nodes", clusterids = 1:length(x$clusters),
                  nodes = NULL, indices, features, default = 15, showall = FALSE)

### Arguments

`x` | An object of class `linkcomm`.
`type` | A character string specifying either `"nodes"` or `"edges"`.
`clusterids` | An integer vector of community IDs that will be plotted. Defaults to all communities.
`nodes` | A character vector specifying node(s) that will be plotted. Overrides `clusterids`. Defaults to NULL.
`indices` | An integer vector specifying the indices of the nodes or edges that will be given specific size or width values. See `getNodesIn` and `getEdgesIn` for ways to generate these indices. Also see examples in `vignette(topic = "linkcomm", package = "linkcomm")`.
`features` | An integer vector specifying the node or edge sizes for the nodes or edges that are to be changed. If there is a single value then this will be applied to all nodes or edges specified in `indices`, otherwise the `features` vector must be the same length as the `indices` vector and the values will be matched to each other.
`default` | An integer value specifying the node size or edge width that all nodes or edges not specified by `indices` will take. Defaults to 15.
`showall` | Logical, whether edges that don't belong to communities will also be plotted or not. Defaults to FALSE.

### Value

A named integer vector of node sizes or edge widths. The names will be either node names or edge indices.

### Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

### References

Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.

### See Also

`plotLinkCommGraph`, `getNodesIn`, `getEdgesIn`, `vignette(topic = "linkcomm", package = "linkcomm")`.

### Examples

    ## Generate graph and extract link communities.
    g <- swiss[,3:4]
    lc <- getLinkCommunities(g)

    ## Make node size vector for all nodes that belong to community 1.
    graph.feature(lc, indices = getNodesIn(lc, type = "indices"), features = 20, default = 5)

    ## Make edge width vector for all edges that belong to community 1.
    graph.feature(lc, type = "edges", indices = getEdgesIn(lc), features = 5, default = 1)

[Package linkcomm version 1.0-14 Index]